Contacts of the strand formed by residues 1449 - 1453 (chain D) in PDB entry 6X34
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TRP1449 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1446D SER 4.2 8.3 - - - -
1447D CYS* 3.3 41.7 - - + -
1448D VAL* 1.3 76.6 + - - +
1450D VAL* 1.3 62.5 + - - +
1464D PHE* 3.4 43.5 - - + -
1465D ASP* 5.3 0.7 - - - -
1466D LEU* 3.4 31.0 - - + +
1494D MET* 3.9 13.5 - - + -
1495D VAL 3.3 23.8 - - - -
1496D TRP* 3.6 26.1 - + - -
1552D VAL* 3.5 0.7 - - - -
1553D PHE* 2.7 69.4 + - + -
1554D VAL 6.1 0.2 - - - -
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Residues in contact with VAL1450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1435D TYR* 4.8 14.1 - - + -
1437D VAL* 3.7 31.9 - - + -
1448D VAL* 4.1 13.9 - - + -
1449D TRP* 1.3 79.2 - - - +
1451D GLY* 1.3 63.4 + - - +
1494D MET* 3.4 4.0 - - - -
1495D VAL* 3.2 25.5 + - - +
1516D ILE* 3.8 21.6 - - + +
1529D PHE* 3.8 9.7 - - + -
1551D ALA 3.7 3.1 - - - +
1552D VAL* 3.8 30.5 - - + -
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Residues in contact with GLY1451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1435D TYR* 5.7 1.4 - - - -
1449D TRP 4.3 0.2 - - - -
1450D VAL* 1.3 79.2 - - - +
1452D TRP* 1.3 66.3 + - - -
1493D TYR 3.2 13.8 + - - -
1529D PHE* 3.7 18.2 - - - -
1550D PRO* 3.6 5.4 - - - +
1551D ALA* 2.8 32.9 + - - +
1553D PHE* 5.6 0.8 - - - -
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Residues in contact with TRP1452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1295D VAL* 3.7 31.4 - - + -
1435D TYR* 4.7 28.0 - + + -
1451D GLY* 1.3 78.7 - - - -
1453D VAL* 1.3 58.7 + - - +
1493D TYR* 2.6 53.0 + - + +
1518D CYS* 5.0 3.6 - - + +
1520D VAL* 3.6 35.0 - - + +
1527D MET* 3.5 25.5 - - + -
1529D PHE* 4.0 22.3 - + - -
1548D LEU* 3.8 17.9 - - + -
1549D PHE 3.2 6.7 - - - -
1550D PRO* 3.5 44.4 - - + -
1551D ALA* 4.9 0.7 - - - -
1575D LEU* 5.7 7.0 - - + -
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Residues in contact with VAL1453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1245D PHE* 5.3 5.8 - - + -
1290D ARG* 3.8 15.9 - - + -
1452D TRP* 1.3 75.8 - - - +
1454D THR* 1.4 72.8 + - - +
1457D TYR* 3.6 32.1 - - + -
1491D ASN 4.0 4.7 - - - +
1492D CYS* 4.2 7.9 - - + +
1493D TYR* 5.9 0.7 - - - +
1548D LEU* 3.3 4.6 - - - -
1549D PHE* 2.5 63.2 + - + +
1551D ALA* 3.6 22.9 - - + -
1553D PHE* 5.2 4.5 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il